We have sat on the plane in Philly waiting for passengers from connecting flights, so they do wait. I also know that they will get the bags for the connecting flight off before the bags that are for people who are not connecting.
Once when we flew to another island, we went the day before to avoid a very early flight, and checked into a hotel with an airport shuttle and free breakfast in Charlotte. We met up with friends, went out to dinner and the next morning went back to the airport. It was much better than the 6 am flight with a long layover.